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| Title | Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State. |
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| Journal, issue, pages | Structure, Vol. 23, Issue 6, Page 1138-1149, Year 2015 |
| Publish date | Jun 2, 2015 |
 Authors | Muhibur Rasheed / Radhakrishna Bettadapura / Chandrajit Bajaj /  |
| PubMed Abstract | Envelope glycoprotein gp120 of HIV-1 possesses several variable regions; their precise structure has been difficult to establish. We report a new model of gp120, in complex with antibodies CD4 and ...Envelope glycoprotein gp120 of HIV-1 possesses several variable regions; their precise structure has been difficult to establish. We report a new model of gp120, in complex with antibodies CD4 and 17b, complete with its variable regions. The model was produced by a computational protocol that uses cryo-electron microscopy (EM) maps, atomic-resolution structures of the core, and information on binding interactions. Our model has excellent fit with EMD: 5020, is stereochemically and energetically favorable, and has the expected binding interfaces. Comparison of the ternary arrangement of the loops in this model with those bound to PGT122 and PGV04 suggested a possible motion of the V1V2 away from the CCR5 binding site and toward CD4. Our study also revealed that the CD4-bound state of the V1V2 loop is not optimal for gp120 bound with several neutralizing antibodies. |
 External links | Structure / PubMed:26039348 / PubMed Central |
| Methods | EM (single particle) |
| Resolution | 20 Å |
| Structure data |  PDB-3j70: |
| Source |
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 Keywords |  VIRAL PROTEIN/IMMUNE SYSTEM / gp120 / V1V2 / CD4 / 17b / VIRAL PROTEIN-IMMUNE SYSTEM complex |
